Preliminary design of low-thrust interplanetary missions is a highly complex process. The mission designer must choose discrete parameters such as the number of flybys, the bodies at which those flybys are performed, and in some cases the final destination. Because low-thrust trajectory design is tightly coupled with systems design, power and propulsion characteristics must be chosen as well. In addition, a time-history of control variables must be chosen which defines the trajectory. There are often many thousands, if not millions, of possible trajectories to be evaluated. The customer who commissions a trajectory design is not usually interested in a point solution, but rather the exploration of the trade space of trajectories between several different objective functions. This can be very expensive process in terms of the number of human analyst hours required. An automated approach is therefore very desirable. This work presents such an approach by posing the mission design problem as a multi-objective hybrid optimal control problem. The methods is demonstrated on hypothetical mission to the main asteroid belt and to Deimos.